After deselecting a folder from the list of folders you choose to sync, you may see an error: "The file or folder already exists on OneDrive."
Option 1: Delete it from the PC.
Note: It’s safe to delete the file because it’s still available in OneDrive online. If you don’t want to have the folder in OneDrive and only have the folder on your PC, move the folder out of the PC’s OneDrive folder (see option 2 below).
Option 2: Remove the file or folder from OneDrive.
Note: With the file included in your list of folders to sync, move the folder to another place outside the OneDrive folder structure. This will delete the files and folder from OneDrive.com and make them only available on your PC.